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Families SA said an order was given two weeks ago for workers to prioritise answering emails, which resulted in wait times of up to an hour for the Child Abuse Report Line.

"It is very difficult to cope in the call centre for child protection workers," said Jan McMahon from the Public Service Association, the union that represents workers at the Families SA.

"I mean, their workload is just through the roof."

Ms McMahon is concerned about the apparent decision at the agency to delay answering the phones.

"It really was a very silly decision by the department to instruct child protection workers not to answer the phone," she said.

"It does puts children at risk."

Families SA has acknowledged that over the past fortnight workers were told to give priority to answering emails, leading to long wait times on the phone.

"It is very important for us still to capture the information in the electronic notifications because they can be as important as a telephone notification," said Etienne Scheepers, who oversees the child protection agency for the South Australian Education Department.

"There was a focus to deal with some of the backlog on electronic notifications during that period."

Mr Scheepers said he could not speculate on the nature of the calls that were left waiting.

"[It's] not our intention to keep people waiting and we apologise if wait for a period that is too long."

In September, Families SA revealed 85,000 phone calls were abandoned to the hotline in the four financial years to June.

An online reporting system was supposed to ease the pressure, but Ms McMahon said workers are still struggling.

"What we see is at many times they have to do administrative work, for example on a night shift they have to respond to emergency situations that involve children," Ms McMahon said.

"That might mean they have to remove them from a home, then they have to find a place where they can be put and often they end up babysitting or caring for these children because there is no support to assist them."

Ms McMahon has called for more staff and resources in the call centre, a sentiment that is echoed by Rachel Sanderson from South Australia's Liberal Opposition.

"Basically they're just shifting the problem, so they've told their staff to focus on the ECAL reports and then put people on hold for an hour," she said.

"So it doesn't solve anything, it just moves the problem around and the Government needs to employ the right amount of people to get on top of their work load and do it properly."

Ms Sanderson said Families SA has had years to improve the practices at the call centre.

"If this was any normal business you would work back until that work got done or you would bring in extra staff to clear the backlog.

"We're not talking about minor issues; these are children whose lives are in danger.

"That people have gone to the effort to report neglect or abuse and the Government are letting these people slip through the cracks."Etienne Scheepers said the agency has added about 10 workers to the call centre in recent months, and is planning to bring in staff with fewer qualifications to ease the burden on social workers.

"We are proposing to have a fully evaluated pilot of non-social worker taking calls," he said.

"That will increase the number of resources within the call centre.

"It will then allow our valuable social worker resources to focus on assessment and not on information taking."

He said some calls can also be made to other welfare agencies rather than the Child Abuse Report Line, and in serious cases, should be made directly to police.